Sitemap and docking
Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock […]
02_Run Maestro, Run Maestro command
[Version: 3.0.0 Requires: only the free node plugin and a Maestro installation for some workflows]
Batch execution 1
Test running the current workflow with KNIME_batch.py.
Conformer cluster
Cluster conformers based on Cartesian or torsional RMSD. [Requires: Maestro, ConfGen]
Parameter flow variables 1
Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the protein preparation, […]
AutoQSAR
Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR nodel to other compounds, with either traditional QSAR methods or […]
Validate parameters 1-2
Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an […]
GroupBy 1-2
Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]
Run PyMOL 1
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]